Investigation of melanoma treatments in mice and humans
Introduction
Dataset and general idea - What we wanted to do and why we chose that dataset - What did we intend to analyse in the datasets - What was our general goal for the project
Methods
Cleaning
- How we cleaned the data and why
Augmentation
- How we processed or data to prepare it for analysis
- Why we did 0 handling and how
- Why we did log2 fold expressions
Results
Mouse gene expression analysis
- Only 346 significantly regulated genes out of 39075
- 0 handling making estimated treatment impact on expressions unsure.
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Analysis of regulated Mouse genes across the 3 treatments
Approximately equal amounts of significantly regulated genes in each treatment
However, the overlap is very small
Discussion
Combined investigation across mouse and human melanoma cell lines provided valuable insights into the influences of the studied compounds and treatment effects on their gene expression patterns
Future work is needed to better understand the impact of these treatments on gene expression and cellular pathways across different melanoma cells ( selection of other promising cell candidates and compounds)
References
Jo Waaler (2022) Human melanoma cell lines treated with G007-LK. BioStudies, E-MTAB-8438. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8438
Jo Waaler (2021). Mouse melanoma cell line B16-F10 treated with G007-LK. BioStudies, E-MTAB-8101. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8101
Waaler, Jo, et al. “Tankyrase Inhibition Sensitizes Melanoma to PD-1 Immune Checkpoint Blockade in Syngeneic Mouse Models.” Communications Biology, vol. 3, no. 1, 24 Apr. 2020, https://doi.org/10.1038%2Fs42003-020-0916-2 Accessed 25 Nov. 2023
Martín‐Fernández, Josep Antoni, Javier Palarea‐Albaladejo, and Ricardo Antonio Olea. “Dealing with zeros.” Compositional data analysis: Theory and applications (2011): 43-58.